NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data.

ABSTRACT:

Background

Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers.

Results

In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purposes. We evaluated SV calling performance of NextSV under different PacBio coverages on two personal genomes, NA12878 and HX1. Our results

SUBMITTER: Fang L 

PROVIDER: S-EPMC5966861 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature